Is this a 5-speed automatic transmission? If so, they were notorious for have shifting issues due to the valve body warping. As far as the EGR, it should be not far from the throttle body. If you go into the "knowledge base" section, you can access the "engine control" section of the factory service manual for your vehicle. It will have the diagnostic steps for your trouble code and should have a picture of the EGR system, as well. I wouldn't think the EGR is causing the transmission issue. If it was stuck closed, it would just trigger the CEL. If it was stuck open, you would get a lean, rough idle. This is an electronic EGR, so it is possible that it could fail electronically rather than just because it is dirty. Following the FSM diagnostics should help isolate the problem.